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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HTqPCR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HTqPCR_1.54.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/HTqPCR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTqPCR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTqPCR’ version ‘1.54.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTqPCR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘Biobase’ ‘limma’ ‘RColorBrewer’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmapSig: warning in heatmap.2(data, trace = "none", density.info =
"none", col = col, distfun = d, breaks = b, mar = mar, ...): partial
argument match of 'mar' to 'margins'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
partial argument match of 'n' to 'number'
limmaCtData: warning in topTable(fit2, sort = "none", n = nrow(fit2)):
partial argument match of 'sort' to 'sort.by'
plotCtCor: warning in heatmap.2(x, col = col, breaks = b, scale =
"none", dendrogram = "row", trace = "none", main = main, density.info
= "none", mar = mar, ...): partial argument match of 'mar' to
'margins'
plotCtHeatmap: warning in heatmap.2(data, trace = "none", density.info
= "none", main = main, col = col, distfun = d, breaks = breaks, mar =
mar, ...): partial argument match of 'mar' to 'margins'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
SD[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra = 0.001):
partial argument match of 'sfra' to 'sfrac'
plotCtOverview: warning in plotCI(x = x.pos + i - 1, y = M[i, ], uiw =
SD.ratio[i, ], add = TRUE, gap = 0, pch = 20, xpd = TRUE, sfra =
0.001): partial argument match of 'sfra' to 'sfrac'
.readCtBioMark: no visible global function definition for ‘read.csv’
.readCtCFX: no visible global function definition for ‘read.csv’
.readCtOpenArray: no visible global function definition for ‘read.csv’
cbind.qPCRset: no visible global function definition for ‘phenoData<-’
cbind.qPCRset: no visible global function definition for
‘AnnotatedDataFrame’
cbind.qPCRset: no visible global function definition for ‘pData’
cbind.qPCRset: no visible global function definition for
‘capture.output’
changeCtLayout: no visible global function definition for
‘featureData<-’
changeCtLayout: no visible global function definition for ‘featureData’
changeCtLayout: no visible global function definition for ‘phenoData<-’
changeCtLayout: no visible global function definition for
‘capture.output’
filterCategory: no visible global function definition for
‘capture.output’
filterCtData: no visible binding for global variable ‘IQR’
filterCtData: no visible global function definition for
‘capture.output’
mannwhitneyCtData : <anonymous>: no visible global function definition
for ‘wilcox.test’
normalizeCtData: no visible global function definition for
‘capture.output’
rbind.qPCRset: no visible global function definition for
‘featureData<-’
rbind.qPCRset: no visible global function definition for
‘AnnotatedDataFrame’
rbind.qPCRset: no visible global function definition for ‘fData’
rbind.qPCRset: no visible global function definition for
‘capture.output’
readCtData: no visible global function definition for
‘AnnotatedDataFrame’
readCtData: no visible global function definition for ‘capture.output’
setCategory: no visible global function definition for ‘capture.output’
[,qPCRset: no visible global function definition for ‘phenoData<-’
[,qPCRset: no visible global function definition for ‘phenoData’
exprs,qPCRset: no visible global function definition for
‘assayDataElement’
exprs<-,qPCRset-ANY: no visible global function definition for
‘assayDataElementReplace’
featureCategory,qPCRset: no visible global function definition for
‘assayDataElement’
featureCategory<-,qPCRset: no visible global function definition for
‘assayDataElementReplace’
featureClass,qPCRset: no visible global function definition for ‘fData’
featureClass<-,qPCRset: no visible global function definition for
‘fData’
featureClass<-,qPCRset: no visible global function definition for
‘fData<-’
featureNames,qPCRset: no visible global function definition for ‘fData’
featureNames<-,qPCRset-character: no visible global function definition
for ‘fData’
featureNames<-,qPCRset-character: no visible global function definition
for ‘fData<-’
featurePos,qPCRset: no visible global function definition for ‘fData’
featurePos<-,qPCRset: no visible global function definition for ‘fData’
featurePos<-,qPCRset: no visible global function definition for
‘fData<-’
featureType,qPCRset: no visible global function definition for ‘fData’
featureType<-,qPCRset: no visible global function definition for
‘fData’
featureType<-,qPCRset: no visible global function definition for
‘fData<-’
flag,qPCRset: no visible global function definition for
‘assayDataElement’
flag<-,qPCRset: no visible global function definition for
‘assayDataElementReplace’
Undefined global functions or variables:
AnnotatedDataFrame IQR assayDataElement assayDataElementReplace
capture.output fData fData<- featureData featureData<- pData
phenoData phenoData<- read.csv wilcox.test
Consider adding
importFrom("stats", "IQR", "wilcox.test")
importFrom("utils", "capture.output", "read.csv")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: cbind.Rd:35-36: Dropping empty section \examples
prepare_Rd: heatmapSig.Rd:31-32: Dropping empty section \examples
prepare_Rd: mannwhitneyCtData.Rd:52-62: Dropping empty section \examples
prepare_Rd: plotCtRQ.Rd:46-48: Dropping empty section \examples
prepare_Rd: plotCtSignificance.Rd:46-47: Dropping empty section \examples
prepare_Rd: ttestCtData.Rd:49-50: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/HTqPCR.Rcheck/00check.log’
for details.
